Correlating haplogroups with ancient admixture

[ElHorsto]

That being said, I also wonder whether some IEans or other might have had 0% "North_European" of any kind and came straight from Anatolia to Italy. Their smaller ANE would show up perhaps as "West_Asian" admixture then.

 

[ElHorsto]

Sicilian 0 of WHG doesn't make sense. Please give me at least 0.001 lol. What happened to WHG from Greeks, Romans, Vandal, or even some tourists from North who settled there. Are you sure sampling wasn't from one village only? (My comical rant and a question are towards scientists of the paper not to you personally)
Sardinian ANE is also suspicious, it should be at least 0.04, and Ashkenazi WHG is ridiculous, at least 0.002 should be more appropriate. We should wait for more samples.

If I understood correctly, the 0% and 100% are predefined limits such that new samples can still exceed these limits. That's why most near-easteners show > 100% EEF and < 0% WHG for instance. This means the "true" range is not exactly known and having 0% of something is more realistic then because 0% is not the border of the "true" unknown range.

If I remember correctly, the authors also state somewhere that the figures for Ashkenazi, Jews and Sicilians are not so useful.

 

[Wilhelm]

You guys don't get it, the Sicilians/Maltese/Jews and also Morodvians/Finns are out of range for this test, since they have additional layers of admixture out of the EEF/WHG/ANE ancestries-. In the first group, is because of near-east ancestry, in the second because of Siberian.

 

[Angela]

If I understood correctly, the 0% and 100% are predefined limits such that new samples can still exceed these limits. That's why most near-easteners show > 100% EEF and < 0% WHG for instance. This means the "true" range is not exactly known and having 0% of something is more realistic then because 0% is not the border of the "true" unknown range.

If I remember correctly, the authors also state somewhere that the figures for Ashkenazi, Jews and Sicilians are not so useful.

Thanks, I had forgotten that the Ashkenazi were included with the Sicilians and some far north-eastern Europeans in that group. I suppose therefore that we really can't draw any conclusions about "European" admixture from the results in this paper.

 

[LeBrok]

If I understood correctly, the 0% and 100% are predefined limits such that new samples can still exceed these limits. That's why most near-easteners show > 100% EEF and < 0% WHG for instance. This means the "true" range is not exactly known and having 0% of something is more realistic then because 0% is not the border of the "true" unknown range.

If I remember correctly, the authors also state somewhere that the figures for Ashkenazi, Jews and Sicilians are not so useful.

Yes I noticed this, it makes sense, but the 0 was confusing for me yesterday. If they gave reading +0.005 or -0.004 that would mean they took a measurement, but 0.00 means they somehow gave up on measuring at all, I guess.

Other thing that might be hiding the complete truth of admixtures is that they (for now) selected people who might not be a pure farmers or pure hunter-gatherers. The samples are from 7-8k years ago. At this time the stuttgart farmer most likely mixed somewhat with local H-Gs and carries already some of WHG admixture. Granted that they call this admixture EEF and not NEF (near eastern farmer). This might skew the results showing less WHG though, or rather native/ancient european component level.

From the paper:

Recognizing the challenge posed by the lack of accurate surrogates for the ancestral populations, we
hypothesized that Stuttgart is a mixture of an unknown hunter-gatherer population that forms a clade
with Loschbour and an unknown Near Eastern population (NE) in proportions 1- and . W

I think I'm going to retract my thoughts that 0.05 level of ANE showing in south europe was brought by near eastern farmers. If any it was already included in EEF, because EEF was 100%=stuttgart sample, and it wouldn't show separately as ANE. Sardinian sample might be a very original of EEF with some later WHG influence.

Part (or maybe most) ANE in south might be of IE (R1b) origin. It spikes in Greece, entry point, and falls to the West as they continue the migration.

 

[LeBrok]

More from paper:

and this suggests
that MA1 and Motala12 share more common drift than MA1 and Loschbour.
Scandinavian hunter-gatherers could indeed be fit if they were modeled as a mixture of Loschbour and MA1.

From article:

Scandinavian Hunter-Gatherer (SHG): this is a meta-population made up of Swedish Mesolithic and Neolithic forager samples from Motala and Gotland, respectively. It's a more easterly variant of WHG, with probable ANE admixture

Now we have to look for SHG in our genome.

 

[epoch]

One final thought before I fall asleep over the computer...the Bollingino study that was cited above made some pretty broad claims based on one incidence of HG's and EEF sharing time and space in central Europe. I don't know if that finding can be extrapolated to the situation over all of Europe, i.e. that there were a lot of HG's who remained basically in place, tending to their fishing and ignoring the farmers tilling the good loess soils. Actually, they were'nt totally ignoring each other. The mtDNA data doesn't show any EEF females being absorbed into the HG community, but a good number of the WHG mtDNA lines did show up among the members of the Neolithic farming community. So, it's those U mtDNA signatures that show that admixture was indeed taking place.

But there is more than just paleogenetics to backup that story. There is the Dutch situation were loess grounds were used by LBK farmers in a small part, yet the hunter-gatherers maintained, even as late as 2600 BC, the Vlaardingen culture. Before, a local agricultural culture evolved which still remained largely hunter-gatherer (It might be good to remember that we all are still hunter-gatherers: We fish the seas, we eat game at Christmas) that was called Swifterband culture. Remains of burials are recovered. We also have Ertebolla culture, from about the same time.

But yes, there is also evidence that they weren't completely ignoring each other. I found a document that states there is some archeological evidence that some of the mesolithic burial rituals were copied at the fringes of the LBK culture, so the more hybrid farmers may simply not have been sampled yet. And even EEF Stuttgart had WHG admixture, as is visible in this:

http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-2.pdf

The big question is, what was the Y signature of these EEF men...G2a, and some I2a, doubtless, and if they were happily outbreeding all the HG males, you would have a big increase in G2a for example. So what happened? Are R1b and R1a, ANE carriers for the sake of the argument, responsible for the decrease in the EEF males lineages? They certainly didn't replace the autosomal make-up of these people however. I read somewhere that the median in Europe is over 56 for EEF.

And here I was thinking that some good ancient DNA would clear everything up? LOL

Y-DNA and mtDNA obviously are more prone to drifts than autosomal DNA. As a thought experiment take a mother with four healthy sons. She will not spread her mtDNA but will contribute largely to the autosomal pool, especially if the sons all take more than one wife.

 

[LeBrok]

Originally Posted by ElHorsto
If I understood correctly, the 0% and 100% are predefined limits such that new samples can still exceed these limits. That's why most near-easteners show > 100% EEF and < 0% WHG for instance. This means the "true" range is not exactly known and having 0% of something is more realistic then because 0% is not the border of the "true" unknown range.

If I remember correctly, the authors also state somewhere that the figures for Ashkenazi, Jews and Sicilians are not so useful.



Yes I noticed this, it makes sense, but the 0 was confusing for me yesterday. If they gave reading +0.005 or -0.004 that would mean they took a measurement, but 0.00 means they somehow gave up on measuring at all, I guess.

My initial suspicion is confirmed in the paper:

While our three-way mixture model fits the data for most European populations, two sets of populations are poor fits. First, Sicilians, Maltese, and Ashkenazi Jews have EEF estimates beyond the 0-100% interval (SI13) and they cannot be jointly fit with other Europeans (SI12). These populations may have more Near Eastern ancestry than can be explained via EEF admixture (SI13), an inference that is also suggested by the fact that they fall in the gap between European and Near Eastern populations in the PCA of Fig. 1B.

 

[Goga]

Wow, that's much lower than I expected for WHG, and ANE not high either. I wonder if the calculator is doing the job right. If I understood correctly, in original paper, scientists used comparable statistics of whole (all they could sequence) genomes of Stuttgart, Loschbour and MA1 (mal'ta boy?). On other hand we amateurs use K13 for calculating admixtures, and from this 3 ancestral groups. It is a shortcut and contains inaccuracies, especially for some populations. Someone correct me if I'm wrong.

According to a modified calculator for West Asians, I've 17.606% of ANE and according to DODECAD K12b calculator I've got only 4.87% of North_European component, 28.04% of Gedrosia and 37.76% of Caucasus component. So ANE in me is for the greatest part correlated with Gedrosia and Caucasus component, I guess.

 

[pyromatic]

probably I1 came from the late I* found in mesolithic Scandinavia.

There was no I* found in mesolithic Sweden. The two samples that weren't I2 were simply I. They did not test any of the SNPs phyloequivalent to M253, none of the SNPs that define I2, I2a, I2b, or I2c; nor did they test all of the I-defining SNPs.

The I2-M423 individuals were subsequently found to be derived for about half and ancestral for the other half of the SNPs phyloequivalent to M423, putting them on a parallel branch to that from which all modern I2-M423 individuals descend, one that has subsequently gone extinct; or they are members of the population that was ancestral to all modern I2-M423. Additionally, the ancient I2-M423 samples shared the same derived/ancestral state on the phyloequivalent SNPs that could be read.

Motala2 and Motala9 are just I. They are not true generics, and, based on the results of the extended testing on the I2 individuals, I suspect Motala2 and Motala9 would similarly be I2.

I1 and pre-I1 are yet to be found in ancient DNA.